exRNAdisease

General Information

Database ID:

exR0000085

RNA Name:

ABHD2

RNA Type:

mRNA

Chromosome:

chr15

Starnd:

Coordinate:

Start Site(bp):

89087459

End Site(bp):

89202355

External Links:

Disease Information

Disease Name:	Down Syndrome
Disease Category:	Congenital, Hereditary, and Neonatal Diseases and Abnormalities
MeSH ID:	D004314
Type:	Diseases Category/Congenital, Hereditary, and Neonatal Diseases and Abnormalities
Alias:	Syndrome, Down//Mongolism//47,XY,+21//Trisomy G//47,XX,+21//Down's Syndrome//Downs Syndrome//Syndrome, Down's//Trisomy 21//Trisomy 21, Mitotic Nondisjunction//Down Syndrome, Partial Trisomy 21//Partial Trisomy 21 Down Syndrome//Trisomy 21, Meiotic Nondisjunction

Expression Detail

GEO ID:	GSE16176
Description:	Expression profiles of amniotic fluid from human fetuses with Down syndrome and euploid controls
Experimental Design:	Disease vs Control
Case Disease Type:	Down Syndrome
Case Disease SubType:	NA
Case Sample:	Down Syndrome
Control Sample:	Normal
Number of Case:	7
Number of Control:	7
Number of Samples:	14

Regulatory Relationship

mRNA targets:

Gene Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
NUP210	chr3	13316235	13420322	-
RPS21	chr20	62387103	62388520	+
RPS6KB2	chr11	67428460	67435401	+
MT-ND5	chrMT	12337	14148	+
PPIF	chr10	79347469	79355334	+
BRD2	chr6	32968594	32981505	+
MMD	chr17	55392622	55421924	-
AP3S2	chr15	89830599	89894638	-
EEF1A1	chr6	73515750	73523797	-
PABPC3	chr13	25095868	25099254	+
MKRN1	chr7	140453033	140479536	-
AC024592.3	chr19	5866171	5903787	-
SHC2	chr19	416583	460996	-
DMWD	chr19	45782947	45792845	-
RPUSD3	chr3	9837849	9844602	-
PTGIS	chr20	49503874	49568137	-
METTL2A	chr17	62423867	62450822	+
EMC3	chr3	9962537	10011116	-
NDUFA11	chr19	5891276	5904006	-
KMT2D	chr12	49018975	49059774	-
CMTM3	chr16	66603874	66613892	+
HLA-A	chr6	29941260	29945884	+
CWC27	chr5	64768930	65018750	+
CCDC174	chr3	14651746	14672659	+
ATP5F1A	chr18	46080248	46104334	-
RNF40	chr16	30761745	30776307	+
MACF1	chr1	39081316	39487177	+
HOXD4	chr2	176151550	176153226	+
TSSC4	chr11	2400488	2403878	+
SALL2	chr14	21521080	21537216	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-15a-5p	chr13	50049167	50049188	-
hsa-miR-103a-3p	chr5	168560904	168560926	-
hsa-miR-107	chr10	89592756	89592778	-
hsa-miR-214-3p	chr1	172138816	172138837	-
hsa-miR-15b-5p	chr3	160404607	160404628	+
hsa-miR-195-5p	chr17	7017667	7017687	-
hsa-miR-497-5p	chr17	7017979	7017999	-
hsa-miR-423-5p	chr17	30117095	30117117	+
hsa-miR-532-3p	chrX	50003204	50003225	+
hsa-miR-541-3p	chr14	101064548	101064569	+
hsa-miR-665	chr14	100875075	100875094	+
hsa-miR-873-5p	chr9	28888925	28888945	-
hsa-miR-1294	chr5	154347153	154347174	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC067930.1	chr8	143579636	143580670	+
AC104257.1	chr8	131308545	131317632	+
AC079949.1	chr12	127142029	127146532	-
MUC20-OT1	chr3	195658062	195739964	+
SNAI3-AS1	chr16	88663298	88687278	+
XIST	chrX	73820649	73852723	-

Display:

Experiment Detail

GEO ID:	GSE16176
Sample Source:	Amniotic Fluid
Source Fraction:	Supernatant
Platform:	GPL570
Method:	Microarray
Num of detected RNA Type:	1
Num of detected RNAs of this Type:	17063
Sample treatment protocol:	NA
RNA Extract protocol:	RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer's protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
RNA library preparation protocol:	biotin Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

Reference

PMID:	19474297
Title:	Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses
Author:	Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW
Journal:	Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9425-9.
Description:	To characterize the differences between second trimester Down syndrome (DS) and euploid fetuses, we used Affymetrix microarrays to compare gene expression in uncultured amniotic fluid supernatant samples.